The Experts below are selected from a list of 201 Experts worldwide ranked by ideXlab platform
Osamu Nakagomi - One of the best experts on this subject based on the ideXlab platform.
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Isolation and molecular characterization of a serotype 9 human rotavirus strain.
Microbiology and Immunology, 2013Co-Authors: Toyoko Nakagomi, Noriko Katsushima, Atsushi Ohshima, Kaoru Akatani, Nobuko Ikegami, Osamu NakagomiAbstract:A human rotavirus strain, designated AU32, that belongs to serotype 9 was isolated and was compared by RNA-RNA Hybridization with recently established two serotype 9 strains (WI61 and F45) as well as other prototype human strains. These three strains exhibited a very high degree of homology with one another and shared a high degree of homology with strains belonging to the Wa genogroup but not with strains belonging to either the DS-1 or AU-1 genogroup. These results suggest that genetic constellation of the serotype 9 strains is similar to that of the commonest human rotavirus despite the recent recognition of this serotype.
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Isolation and molecular characterization of a naturally occurring non-structural protein 5 (NSP5) gene reassortant of group a rotavirus of serotype G2P[4] with a long RNA pattern
Journal of medical virology, 2005Co-Authors: Kamruddin Ahmed, Toyoko Nakagomi, Osamu NakagomiAbstract:We report here two unusual strains of group A rotavirus, AU85 and AU102, isolated from children with diarrhea. These strains showed an unusual combination of serotype G2 and a long RNA pattern. RNA-RNA Hybridization assays showed that these strains are reassortants in which a single genome segment 11 (the NSP5 gene) was derived from a Wa genogroup strain, while other 10 genome segments from a DS-1 genogroup strain. Phylogenetic analysis showed that the NSP5 gene of strain AU85 did not form cluster with Wa strain, while it belonged to the cluster of YM and other porcine strains. Phylogenetic analysis also showed that NSP5 and VP7 genes of AU85 were derived from the rotavirus circulating in the area. Both co-electrophoresis and RNA-RNA Hybridization showed that AU85 and AU102 are identical strains. Moreover, the nucleotide sequence comparison between these two strains revealed that they had 100% identical NSP4, NSP5, and VP7 genes. These results suggest that AU85 was a reassortant formed relatively recently between rotaviruses belonging to the Wa and the DS-1 genogroup.
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Characterization of Serotype G9 Rotavirus Strains Isolated in the United States and India from 1993 to 2001
Journal of clinical microbiology, 2003Co-Authors: A. R. Laird, Osamu Nakagomi, Toyoko Nakagomi, J. R. Gentsch, Roger I. GlassAbstract:The emergence of rotavirus serotype G9 as a possible fifth globally common serotype in the last decade, together with its increasing detection in association with various genome constellations, raises questions about the origins and epidemiological importance of recent G9 isolates. We examined a collection of 40 G9 strains isolated in the United States from 1996 to 2001 and in India since 1993 to determine their VP7 gene sequences, P types, E types, subgroup specificities, and RNA-RNA Hybridization profiles. With the exception of two U.S. strains, all of the study strains shared high VP7 gene sequence homology (
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Genomic RNA constellation of recently emerging serotype G14 equine rotavirus strains in Japan that is highly homologous with prototype G3 and G14 strains previously identified in the United States of America.
Archives of virology, 2003Co-Authors: Toyoko Nakagomi, Hiroshi Tsunemitsu, Hiroshi Imagawa, Osamu NakagomiAbstract:Serotype G14 was once considered to be uncommon among equine rotaviruses. While it sporadically emerged in some parts of the world, serotype G14 became the dominant G serotype among rotaviruses detected in foals with diarrhea in Japan in the late 1990s. However, it is not known how such recently emerging G14 rotaviruses are related in their overall genomic RNA constellation to prototype G14 strain identified earlier in the United States of America or how they were generated and why they have dominated over G3 equine rotaviruses. Genogrouping by RNA–RNA Hybridization revealed that recently emerging serotype G14 equine rotavirus strains had an overall genomic RNA constellation that was highly conserved not only with contemporary and earlier G3 strains in Japan but also with prototype G3 and G14 strains previously identified in the United States of America. Japanese G14 rotavirus strains are likely to have originated form a VP7 gene substitution reassortant that had been formed earlier in the United States of America on the background of the then dominant G3 equine rotavirus.
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Genogroup characterization of reemerging serotype G9 human rotavirus strain 95H115 in comparison with earlier G9 and other human prototype strains.
Microbiology and immunology, 2002Co-Authors: Toyoko Nakagomi, Osamu NakagomiAbstract:Serotype G9 human rotaviruses have emerged globally since the mid-1990s. The 95H115 strain was derived from a stool specimen collected in Japan in the 1994-95 season, thus it is the earliest of the globally reemerging G9 human rotaviruses that were adapted to cell culture. Genogrouping by RNA-RNA Hybridization was performed to examine the genetic background of 95H115. The 95H115 strain belonged to the Wa genogroup, the most common human rotavirus genogroup, and it had a high degree of homology with AU32 and WI61, the prototype G9 isolates in the 1980s. However, the divergent genomic RNA constellation as indicated by the aberrant Hybridization patterns between 95H115 and earlier G9 strains served as further evidence that 95H115 was not a direct descendant of the prototype strains in the '80s.
T. Nakagomi - One of the best experts on this subject based on the ideXlab platform.
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Human rotavirus HCR3 possesses a genomic RNA constellation indistinguishable from that of feline and canine rotaviruses
Archives of Virology, 2000Co-Authors: T. Nakagomi, O. NakagomiAbstract:Infection and spread of group A rotaviruses under natural conditions are mostly limited to one animal host species. However, rare molecular evidence exists for interspecies transmission by whole virions of animal rotaviruses to humans. Human rotavirus strain HCR3, which was isolated in 1984 from a healthy infant in Philadelphia, U.S.A. was shown by RNA-RNA Hybridization to form 11 hybrid bands with feline rotavirus strain FRV64 and canine rotavirus strains CU-1 and K9, but not with rotaviruses commonly found in humans. Thus, HCR3 was concluded to be originally a rotavirus circulating in cats and dogs and accidental interspecies transmission by whole virions to humans was likely to have occurred in the past.
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Isolation of serotype G8, P6[1] bovine rotavirus from adult cattle with diarrhea.
Journal of clinical microbiology, 1997Co-Authors: M Sato, T. Nakagomi, K Tajima, K Ezura, H Akashi, Osamu NakagomiAbstract:Two electrophoretically identical strains of group A rotavirus were isolated from diarrheic cows aged 3, 4, and 7 years on a dairy farm in Japan. They had a rare serotype combination of G8 and P6[1] and were shown by RNA-RNA Hybridization to be most closely related to bovine strain NCDV-Lincoln (G6P6[1]).
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Molecular epidemiology of human rotaviruses: genogrouping by RNA-RNA Hybridization
Archives of virology. Supplementum, 1996Co-Authors: O. Nakagomi, T. NakagomiAbstract:RNA-RNA Hybridization performed under high stringency conditions allows rotavirus isolates to be grouped together based on the overall similarity of their genomic RNA constellation. Classification by this scheme has been termed “genogrouping”. Genogrouping has advanced molecular epidemiology of human rotaviruses. Major observations include (i) Interspecies transmission occurs in nature and (ii) Intergenogroup reassortment occurs in nature with or without exchange of serotype-determining genes. Genogrouping is a particularly valuable asset for determining the gene constellation of unusual rotavirus isolates.
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Subgroup I serotype 3 human rotavirus strains with long RNA pattern as a result of naturally occurring reassortment between members of the bovine and AU-1 genogroups.
Archives of virology, 1992Co-Authors: O. Nakagomi, E Kaga, G Gerna, A Sarasini, T. NakagomiAbstract:Two human rotavirus strains, PCP 5 and MZ 58, which possessed an unusual combination of subgroup (I), serotype (3) and RNA pattern (long) were examined by RNA-RNA Hybridization to determine their genogroup. While these two strains did not belong to either the Wa or the DS-1 genogroup, PCP 5 and MZ 58 possessed seven gene segments that formed hybrids with bovine rotavirus strain NCDV and four gene segments that formed hybrids with human rotavirus strain AU-1. These results suggest that PCP 5 and MZ 58 were intergenogroup reassortants formed in nature between a member of the bovine rotavirus genogroup and a member of the AU-1 genogroup.
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Human rotavirus strain with unique VP4 neutralization epitopes as a result of natural reassortment between members of the AU-1 and Wa genogroups.
Archives of virology, 1992Co-Authors: O. Nakagomi, E Kaga, T. NakagomiAbstract:Human rotavirus strain K8, which possesses unique VP4 neutralization epitopes, was examined by RNA-RNA Hybridization to determine its genogroup. While it possessed four gene segments that formed hybrids with strain Wa (a prototype of the Wa genogroup), strain K8 possessed seven gene segments, including gene segment 4, that formed hybrids with strain AU-1 (a prototype of the AU-1 genogroup) which has been shown to share a unique gene 4 allele with feline rotaviruses. These results suggest that strain K8 is an intergenogroup reassortant formed in nature between a member of the Wa genogroup and a member of the AU-1 genogroup.
O. Nakagomi - One of the best experts on this subject based on the ideXlab platform.
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Human rotavirus HCR3 possesses a genomic RNA constellation indistinguishable from that of feline and canine rotaviruses
Archives of Virology, 2000Co-Authors: T. Nakagomi, O. NakagomiAbstract:Infection and spread of group A rotaviruses under natural conditions are mostly limited to one animal host species. However, rare molecular evidence exists for interspecies transmission by whole virions of animal rotaviruses to humans. Human rotavirus strain HCR3, which was isolated in 1984 from a healthy infant in Philadelphia, U.S.A. was shown by RNA-RNA Hybridization to form 11 hybrid bands with feline rotavirus strain FRV64 and canine rotavirus strains CU-1 and K9, but not with rotaviruses commonly found in humans. Thus, HCR3 was concluded to be originally a rotavirus circulating in cats and dogs and accidental interspecies transmission by whole virions to humans was likely to have occurred in the past.
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molecular and serologic characterization of novel serotype g8 human rotavirus strains detected in blantyre malawi
Virology, 2000Co-Authors: Toyoko Nakagomi, O. Nakagomi, Nigel A. Cunliffe, Jon R. Gentsch, C D Kirkwood, Jailosi S Gondwe, Winifred Dove, Yasutaka HoshinoAbstract:Abstract During a 2-year study of diarrhea among children in Blantyre, Malawi, greater than 50% of rotavirus strains genotyped by using reverse transcription—polymerase chain reaction possessed previously unrecognized combinations of the neutralization proteins VP7 and VP4. Serotype G8 rotaviruses, which have been identified recently in several African countries, were found to possess P[4] or P[6] VP4 genotype specificity. Two of these short electropherotype rotaviruses were further investigated: these comprised a P[6], G8 representative strain (MW23) and a P[4], G8 representative strain (MW333). The VP7 gene sequences of both strains exhibited greatest homology to human and animal serotype G8 rotaviruses. Sequence analysis of the VP4 gene of MW23 indicated closest identity to the P2A[6], G9 strain US1205 from the United States. The VP4 gene of MW333 was most closely related to the P[4], G12 strain L26 isolated in the Philippines and the Australian P[4], G2 strain RV-5. The NSP4 gene sequences of both strains were classified in NSP4 genetic group I. RNA-RNA Hybridization demonstrated that each of these two strains is related to the DS-1 genogroup of human rotaviruses. Subgroup analysis and virus neutralization confirmed complete antigenic characterization of MW23 as subgroup I, P2A[6], G8 and MW333 as subgroup I, P1B[4], G8. The similarity of the VP7 gene sequences of the prototype strains described in this report to bovine serotype G8 rotaviruses suggests that they may represent human/bovine reassortant viruses.
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Three forms of AU-1 like human rotaviruses differentiated by their overall genomic constellation and by the sequence of their VP8*
Archives of Virology, 1998Co-Authors: R. Gollop, O. Nakagomi, I. Silberstein, L. M. Shulman, H. B. Greenberg, E. Mendelson, I. ShifAbstract:Insight into the origin of human rotaviruses carrying the AU-1 VP4 allele was gained by examining their genomic RNA constellation using RNA–RNA Hybridization and by sequencing the VP8^* portion (nucleotides 1–750) of their gene 4. AU-1 like viruses isolated in Israel from children attending outpatient clinics were classified into three sub-genogroups based on RNA–RNA Hybridization analysis: Subgenogroup 1 consists of two strains (Ro-5829 and Ro-5960) which belong to the AU-1 genogroup, since all their 11 segments hybridized to AU-1 segments. Subgenogroup 2 consists of one reassortant virus (Ro-5193) of which seven RNA segments hybridized to AU-1 segments and the remaining four segments hybridized to NCDV (bovine rotavirus). Subgenogroup 3 consists of four reassortant viruses (Ro-6460, Ro-6584, Ro-6784 and Ro-7044) which had a common genome constellation: only four of their RNA segments hybridized to AU-1 and the other seven segments hybridized to NCDV segments. Sequence analysis of the VP8^* gene also revealed a three level pattern of homology with the AU-1 prototype and the local AU-1-like strains which was consistent with the overall genomic (RNA–RNA) constellation: Subgenogroup 1 had 98–98.1% homology with the AU-1 prototype; Subgenogroup 2 had 96.8% homology with the AU-1 prototype and 95.6–96.7% homology with Subgenogroup 1; Subgenogroup 3 had 95.3–95.6% homology with the prototype AU-1 and 93.4–94.3% homology with Subgenogroup 1. Possible evolutionary pathways are discussed.
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Characterization of human rotavirus genotype P[8]G5 from Brazil by probe-Hybridization and sequence
Archives of Virology, 1996Co-Authors: A. A. Alfieri, E Kaga, O. Nakagomi, J. P. G. Leite, P. A. Woods, R. I. Glass, J. R. GentschAbstract:We report the molecular characterization of rotavirus genotype P[8]G5 strains found in fecal specimens collected in four different regions of Brazil, using digoxigenin (dig)-labeled oligonucleotide probes, sequence analysis, and RNA-RNA Hybridization. The closest sequence relationships of the neutralization antigens of these strains were to the VP4 protein of P1A[8]G1 strain KU (93.3% identity in amino acids 11 to 282) and to the VP7 protein of G serotype 5 strain OSU (87.6% identity in amino acids 8 to 232). Based on VP7 sequence differences, we designed dig-probes that allowed us to discriminate porcine OSU-like strains from G5 strains isolated from Brazilian infants. The genetic relationships of two P[8]G5 isolates to other rotavirus genogroups were analyzed by RNA-RNA Hybridization with [^32P]-GTP probes representative of serotypes P1A[8]G1 (Wa), P[8]G3 (AU17), and P9[7]G5 (OSU). The Brazilian P[8]G5 strains showed sequence homology with genes of Wa-like and OSU-like strains, suggesting that these two strains were naturally occurring reassortants between members of the Wa and porcine rotavirus genogroups. The identification of these strains in diverse geographic areas of Brazil underscores their stability and demonstrates the emergence of clinically important rotavirus diarrhea strains by reassortment.
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Molecular epidemiology of human rotaviruses: genogrouping by RNA-RNA Hybridization
Archives of virology. Supplementum, 1996Co-Authors: O. Nakagomi, T. NakagomiAbstract:RNA-RNA Hybridization performed under high stringency conditions allows rotavirus isolates to be grouped together based on the overall similarity of their genomic RNA constellation. Classification by this scheme has been termed “genogrouping”. Genogrouping has advanced molecular epidemiology of human rotaviruses. Major observations include (i) Interspecies transmission occurs in nature and (ii) Intergenogroup reassortment occurs in nature with or without exchange of serotype-determining genes. Genogrouping is a particularly valuable asset for determining the gene constellation of unusual rotavirus isolates.
Donald H. Burke - One of the best experts on this subject based on the ideXlab platform.
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A Fluorescent Split Aptamer for Visualizing RNA–RNA Assembly In Vivo
ACS synthetic biology, 2017Co-Authors: Khalid K. Alam, Kwaku D. Tawiah, Matthew F. Lichte, David Porciani, Donald H. BurkeAbstract:RNA–RNA assembly governs key biological processes and is a powerful tool for engineering synthetic genetic circuits. Characterizing RNA assembly in living cells often involves monitoring fluorescent reporter proteins, which are at best indirect measures of underlying RNA–RNA Hybridization events and are subject to additional temporal and load constraints associated with translation and activation of reporter proteins. In contrast, RNA aptamers that sequester small molecule dyes and activate their fluorescence are increasingly utilized in genetically encoded strategies to report on RNA-level events. Split-aptamer systems have been rationally designed to generate signal upon Hybridization of two or more discrete RNA transcripts, but none directly function when expressed in vivo. We reasoned that the improved physiological properties of the Broccoli aptamer enable construction of a split-aptamer system that could function in living cells. Here we present the Split-Broccoli system, in which self-assembly is n...
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A Fluorescent Split Aptamer for Visualizing RNA-RNA Assembly In Vivo
2017Co-Authors: Khalid K. Alam, Kwaku D. Tawiah, Matthew F. Lichte, David Porciani, Donald H. BurkeAbstract:RNA-RNA assembly governs key biological processes and is a powerful tool for engineering synthetic genetic circuits. Characterizing RNA assembly in living cells often involves monitoring fluorescent reporter proteins, which are at best indirect measures of underlying RNA-RNA Hybridization events and are subject to additional temporal and load constraints associated with translation and activation of reporter proteins. In contrast, RNA aptamers that sequester small molecule dyes and activate their fluorescence are increasingly utilized in genetically-encoded strategies to report on RNA-level events. Split-aptamer systems have been rationally designed to generate signal upon Hybridization of two or more discrete RNA transcripts, but none directly function when expressed in vivo. We reasoned that the improved physiological properties of the Broccoli aptamer enable construction of a split-aptamer system that could function in living cells. Here we present the Split-Broccoli system, in which self-assembly is nucleated by a thermostable, three-way junction RNA architecture and fluorescence activation requires both strands. Functional assembly of the system approximately follows second order kinetics in vitro and improves when cotranscribed, rather than when assembled from purified components. Split-Broccoli fluorescence is digital in vivo and retains functional modularity when fused to RNAs that regulate circuit function through RNA-RNA Hybridization, as demonstrated with an RNA Toehold switch. Split-Broccoli represents the first functional split-aptamer system to operate in vivo. It offers a genetically-encoded and nondestructive platform to monitor and exploit RNA-RNA Hybridization, whether as an all-RNA, stand-alone AND gate or as a tool for monitoring assembly of RNA-RNA hybrids.
E Kaga - One of the best experts on this subject based on the ideXlab platform.
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Characterization of human rotavirus genotype P[8]G5 from Brazil by probe-Hybridization and sequence
Archives of Virology, 1996Co-Authors: A. A. Alfieri, E Kaga, O. Nakagomi, J. P. G. Leite, P. A. Woods, R. I. Glass, J. R. GentschAbstract:We report the molecular characterization of rotavirus genotype P[8]G5 strains found in fecal specimens collected in four different regions of Brazil, using digoxigenin (dig)-labeled oligonucleotide probes, sequence analysis, and RNA-RNA Hybridization. The closest sequence relationships of the neutralization antigens of these strains were to the VP4 protein of P1A[8]G1 strain KU (93.3% identity in amino acids 11 to 282) and to the VP7 protein of G serotype 5 strain OSU (87.6% identity in amino acids 8 to 232). Based on VP7 sequence differences, we designed dig-probes that allowed us to discriminate porcine OSU-like strains from G5 strains isolated from Brazilian infants. The genetic relationships of two P[8]G5 isolates to other rotavirus genogroups were analyzed by RNA-RNA Hybridization with [^32P]-GTP probes representative of serotypes P1A[8]G1 (Wa), P[8]G3 (AU17), and P9[7]G5 (OSU). The Brazilian P[8]G5 strains showed sequence homology with genes of Wa-like and OSU-like strains, suggesting that these two strains were naturally occurring reassortants between members of the Wa and porcine rotavirus genogroups. The identification of these strains in diverse geographic areas of Brazil underscores their stability and demonstrates the emergence of clinically important rotavirus diarrhea strains by reassortment.
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Serotype G6 human rotavirus sharing a conserved genetic constellation with natural reassortants between members of the bovine and AU-1 genogroups
Archives of Virology, 1994Co-Authors: M. Iizuka, E Kaga, G Gerna, M. Chiba, O. Masamune, O. NakagomiAbstract:Serotype G6 human rotavirus PA151 was examined by RNA-RNA Hybridization in comparison with another G6 strain PA169 and two naturally-occurring G3 reassortants PCP5 and MZ58. PA151 possessed three gene segments that formed hybrids with AU-1 and seven gene segments that formed hybrids with bovine rotavirus NCDV. PA151 also possessed eight, 10 and 10 gene segments that formed hybrids with genomic RNAs from PA169, PCP5, and MZ58, respectively. Thus, PA151 was an intergenogroup reassortant formed in nature between members of the bovine and AU-1 genogroups and it shared a genome constellation with PA169, PCP5, and MZ58. These results suggest that naturally-occurring intergenogroup reassortants possessing such a genome constellation were perpetuated in human populations.
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Naturally occurring dual infection with human and bovine rotaviruses as suggested by the recovery of G1P8 and G1P5 rotaviruses from a single patient.
Archives of virology, 1994Co-Authors: Osamu Nakagomi, Yuji Isegawa, David R Knowlton, Toyoko Nakagomi, R L Ward, E Kaga, S UedaAbstract:Culture adaptation of rotaviruses from an infant with severe diarrhea in Cincinnati, Ohio, yielded not only a virus with the original RNA electropherotype (CJN) but also rotaviruses with other electropherotypes, the most dominant of which was called CJN-M [Ward RL, Knowlton DR, Schiff GM, Hoshino Y, Greenberg HB (1988) in J Virol 62: 1543-1549]. RNA-RNA Hybridization and sequencing studies indicated that CJN was a typical G1P8 human rotavirus while CJN-M was a G1P5 strain and contained four gene segments (including segment 4) of a bovine rotavirus. Thus, the infant was apparently dually infected with human and bovine rotaviruses.
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Thermal degradation of RNA-RNA hybrids during Hybridization in solution.
Molecular and cellular probes, 1992Co-Authors: E Kaga, Osamu Nakagomi, Shiro UesugiAbstract:Degradation of single-stranded RNA molecules at high temperatures was examined in relation to the kinetics of RNA-RNA Hybridization in solution. Eleven species (ranging from 670 bases to 3300 bases) of single-stranded RNAs transcribed from rotavirus genomic RNAs degraded significantly after 16 h of incubation at 65 degrees C. The Hybridization of these 11 RNA molecules to the corresponding genomic RNAs, however, was completed within 30 min of incubation. Partially homologous hybrids that were once formed at an early time of incubation gradually degraded in proportion to the length of incubation at 65 degrees C. Thus, the length of Hybridization has a critical effect on the final Hybridization results. Furthermore, thermal hydrolysis of single-stranded RNA molecules provides a plausible explanation why the percent of nucleotide sequence mismatch allowed to form a stable hybrid in the RNA-RNA Hybridization assays for rotavirus genes is much less than that predicted by calculation.
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Subgroup I serotype 3 human rotavirus strains with long RNA pattern as a result of naturally occurring reassortment between members of the bovine and AU-1 genogroups.
Archives of virology, 1992Co-Authors: O. Nakagomi, E Kaga, G Gerna, A Sarasini, T. NakagomiAbstract:Two human rotavirus strains, PCP 5 and MZ 58, which possessed an unusual combination of subgroup (I), serotype (3) and RNA pattern (long) were examined by RNA-RNA Hybridization to determine their genogroup. While these two strains did not belong to either the Wa or the DS-1 genogroup, PCP 5 and MZ 58 possessed seven gene segments that formed hybrids with bovine rotavirus strain NCDV and four gene segments that formed hybrids with human rotavirus strain AU-1. These results suggest that PCP 5 and MZ 58 were intergenogroup reassortants formed in nature between a member of the bovine rotavirus genogroup and a member of the AU-1 genogroup.
